GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpS in Pseudomonas putida KT2440

Align GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate PP_2261 PP_2261 Sugar ABC transporter, ATP-binding protein

Query= TCDB::G3LHY8
         (358 letters)



>FitnessBrowser__Putida:PP_2261
          Length = 365

 Score =  155 bits (392), Expect = 2e-42
 Identities = 99/307 (32%), Positives = 161/307 (52%), Gaps = 5/307 (1%)

Query: 13  ADYHIYPTDLVLERGTLNVLLGPTLAGKTSLMRLMAGLDRPTGGSIHFDGTDVTGMPVQK 72
           ADY ++  + V E+G    LLGP+  GK++L+ +++GL  P+ G + FDG  V  +  Q 
Sbjct: 21  ADYALHALEHVWEQGGAYALLGPSGCGKSTLLNIISGLLTPSHGEVLFDGKPVNQLSPQA 80

Query: 73  RNVAMVYQQFINYPALTVYNNIASPMRISGKDAATIDREVRKAAELLKLTPYLDRTPLNL 132
           RN+A V+Q  + Y  +TV++N+A P+R  G D A +   V + AE+L+LT  L +   NL
Sbjct: 81  RNIAQVFQFPVVYDTMTVFDNLAFPLRNQGLDEARVRARVEEIAEVLELTAVLRKKARNL 140

Query: 133 SGGQQQRTALARALVK-NASLVLMDEPLANLDYKLREELREELPKIFAQSGAIFVYATTE 191
           +  ++Q+ ++ R LV+ + S +L DEPL  +D  L+ +LR +L +I  Q     +Y T +
Sbjct: 141 TADEKQKVSMGRGLVRDDVSAILFDEPLTVIDPHLKWKLRRKLKQIHEQFNITMIYVTHD 200

Query: 192 PSEALLLGGNTATLNQGRVTQFGPTIEVYRRPVNLATAGIFADPPLNTLDV-TKSGNVFT 250
             EA       A ++ GR+ QFG   E++ RP +         P +N +DV  ++G V  
Sbjct: 201 QLEASTFADKIAVMHGGRIVQFGTPRELFERPRHTFVGYFIGSPGMNLIDVRAEAGAVVF 260

Query: 251 RPSGVTIP--VPSHLAVVPDGPVTIAFHPHHLGLAPQTGDAARLQARTLVSEITGSESFV 308
               + +P  +   LA +  G + +   P  + L     + A   AR L  E  G+   V
Sbjct: 261 GDVQLVLPDGLCERLASLAGGRLQVGIRPEFVQLWDSPFEGA-YPARVLDVEDLGTYRIV 319

Query: 309 HLEYDGV 315
            LE  GV
Sbjct: 320 TLELGGV 326


Lambda     K      H
   0.319    0.136    0.392 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 302
Number of extensions: 14
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 358
Length of database: 365
Length adjustment: 29
Effective length of query: 329
Effective length of database: 336
Effective search space:   110544
Effective search space used:   110544
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory